Davinson Sanchez's injury-time header condemned Watford to a sixth consecutive defeat to increase the pressure on Claudio Ranieri and close the gap on the top four to two points.
A medical emergency in the crowd ensured eight minutes was added on to the second half and that was enough for Antonio Conte's men to break the deadlock with Son's curling free-kick after 97 minutes getting a vital touch of Sanchez after it had sailed over Francisco Sierralta.
Cruelly, it denied Watford a first clean sheet of the season after their star man Emmanuel Dennis was substituted at half-time.